celaref
Single-cell RNAseq cell cluster labelling by reference
Bioconductor version: 3.24 · Package version: 1.31.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
After the clustering step of a single-cell RNAseq experiment, this package aims to suggest labels/cell types for the clusters, on the basis of similarity to a reference dataset. It requires a table of read counts per cell per gene, and a list of the cells belonging to each of the clusters, (for both test and reference data).
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("celaref")Details
| Maintainer | Sarah Williams <sarah.williams1@monash.edu> |
| Author | Sarah Williams [aut, cre] |
| License | GPL-3 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | SingleCell, Software |
| Package Short Url | https://bioconductor.org/packages/celaref/ |
Citation
From within R, enter citation("celaref"):
Sarah Williams. celaref: Single-cell RNAseq cell cluster labelling by reference. doi:10.18129/B9.bioc.celaref, R package version 1.31.0, https://bioconductor.org/packages/celaref.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | celaref_1.31.0.tar.gz |
| Windows binary (x86_64) | celaref_1.31.0.zip |
| macOS binary (arm64) | celaref_1.31.0.tgz |
| macOS binary (x86_64) | celaref_1.31.0.tgz |
Dependencies
Depends: R (>= 3.5.0), SummarizedExperiment
Imports: MAST, ggplot2, Matrix, dplyr, magrittr, stats, utils, rlang, BiocGenerics, S4Vectors, readr, tibble, DelayedArray
Suggests: limma, parallel, knitr, rmarkdown, ExperimentHub, testthat